def numberGenesDetectedCufflinks(infile, outfile):
'''Count no genes detected at copynumer > 0 in each sample'''
table = P.toTable(infile)
attach = '''attach "%(ANN_DATABASE)s" as anndb''' % globals()
statement = '''select distinct c.*, gene_biotype from %(table)s c
inner join anndb.gene_info i
on c.tracking_id=i.gene_id
''' % locals()
df = DB.fetch_DataFrame(statement, DATABASE, attach)
# snip off the cufflinks replicate field
df.columns = [x[:-len("_0")] if x.endswith("_0") else x
for x in df.columns]
melted_df = pd.melt(df, id_vars=["tracking_id", "gene_biotype"])
grouped_df = melted_df.groupby(["gene_biotype", "variable"])
agg_df = grouped_df.agg({"value": lambda x:
np.sum([1 for y in x if y > 0])})
agg_df.reset_index(inplace=True)
count_df = pd.pivot_table(agg_df, index="variable",
values="value", columns="gene_biotype")
count_df["total"] = count_df.apply(np.sum, 1)
count_df["sample_id"] = count_df.index
count_df.to_csv(outfile, index=False, sep="\t")
def numberGenesDetectedFeatureCounts(infile, outfile):
'''Count no genes detected by featureCount at counts > 0 in each sample'''
table = P.toTable(infile)
attach = '''attach "%(ANN_DATABASE)s" as anndb''' % globals()
statement = '''select distinct h.*, gene_biotype from %(table)s h
inner join anndb.gene_info i
on h.gene_id=i.gene_id
''' % locals()
melted_df = DB.fetch_DataFrame(statement, DATABASE, attach)
grouped_df = melted_df.groupby(["gene_biotype", "track"])
agg_df = grouped_df.agg({"counts": lambda x:
np.sum([1 for y in x if y > 0])})
agg_df.reset_index(inplace=True)
count_df = pd.pivot_table(agg_df, index="track",
values="counts", columns="gene_biotype")
count_df["total"] = count_df.apply(np.sum, 1)
count_df["sample_id"] = count_df.index
count_df.to_csv(outfile, index=False, sep="\t")
def numberGenesDetectedFeatureCounts(infile, outfile):
'''Count no genes detected by featureCount at counts > 0 in each sample'''
table = P.toTable(infile)
attach = '''attach "%(ANN_DATABASE)s" as anndb''' % globals()
statement = '''select distinct h.*, gene_biotype from %(table)s h
inner join anndb.gene_info i
on h.gene_id=i.gene_id
''' % locals()
melted_df = DB.fetch_DataFrame(statement, DATABASE, attach)
grouped_df = melted_df.groupby(["gene_biotype", "track"])
agg_df = grouped_df.agg(
{"counts": lambda x: np.sum([1 for y in x if y > 0])})
agg_df.reset_index(inplace=True)
count_df = pd.pivot_table(agg_df,
index="track",
values="counts",
columns="gene_biotype")
count_df["total"] = count_df.apply(np.sum, 1)
count_df["sample_id"] = count_df.index
count_df.to_csv(outfile, index=False, sep="\t")
def numberGenesDetectedCufflinks(infile, outfile):
'''Count no genes detected at copynumer > 0 in each sample'''
table = P.toTable(infile)
attach = '''attach "%(ANN_DATABASE)s" as anndb''' % globals()
statement = '''select distinct c.*, gene_biotype from %(table)s c
inner join anndb.gene_info i
on c.tracking_id=i.gene_id
''' % locals()
df = DB.fetch_DataFrame(statement, DATABASE, attach)
# snip off the cufflinks replicate field
df.columns = [
x[:-len("_0")] if x.endswith("_0") else x for x in df.columns
]
melted_df = pd.melt(df, id_vars=["tracking_id", "gene_biotype"])
grouped_df = melted_df.groupby(["gene_biotype", "variable"])
agg_df = grouped_df.agg(
{"value": lambda x: np.sum([1 for y in x if y > 0])})
agg_df.reset_index(inplace=True)
count_df = pd.pivot_table(agg_df,
index="variable",
values="value",
columns="gene_biotype")
count_df["total"] = count_df.apply(np.sum, 1)
count_df["sample_id"] = count_df.index
count_df.to_csv(outfile, index=False, sep="\t")
def generatePeakSets(infile, outfiles):
outf_con, outf_opt = outfiles
# retrieve maximum number of peaks obtained from inter-replicate IDR
# (table created by loadNPeaksForIndividualReplicates)
statement = ("SELECT"
" Experiment,"
" max(n_peaks) AS nPeaks"
" FROM individual_replicates_nPeaks"
" GROUP BY experiment")
df = Database.fetch_DataFrame(statement, dbhandle=PARAMS['database_name'])
# reassign experiment as index
df = df.set_index("Experiment")
# retrieve number of peaks obtained from pooled_pseudoreplicate IDR
# (table created by loadNPeaksForPooledPseudoreplicates)
statement = ("SELECT"
" Experiment,"
" n_peaks AS nPeaks"
" FROM pooled_pseudoreplicates_nPeaks")
df2 = Database.fetch_DataFrame(statement, dbhandle=PARAMS['database_name'])
# reassign experiment as index
df2 = df2.set_index("Experiment")
# split the infile name to obtain experiment
sample_id = os.path.basename(infile).split("_VS_")[0]
sample = sample_id.split("-")
experiment = "_".join([sample[0], sample[1]])
# retrieve max_numPeaks for experiment
nPeaks = int(df.loc[experiment])
# retrieve numPeaks_Rep0 for experiment
nPeaks_rep0 = int(df2.loc[experiment])
# retrieve maximumn of the two
nPeaks_max = max(nPeaks, nPeaks_rep0)
# establish which column to sort by
if PARAMS["idr_options_ranking_measure"] == "signal.value":
sort_statement = "sort -k7nr,7nr"
elif PARAMS["idr_options_ranking_measure"] == "p.value":
sort_statement = "sort -k8nr,8nr"
elif PARAMS["idr_options_ranking_measure"] == "q.value":
sort_statement = "sort -k9nr,9nr"
else:
raise ValueError("Unrecognised ranking_measure"
" %s don't know which column"
" to sort on" % PARAMS["idr_options_ranking_measure"])
# sort infile by column and write top nPeaks to outfile (conservative)
ignore_pipe_errors = True
statement = ("zcat %(infile)s |"
" %(sort_statement)s |"
" head -%(nPeaks)s |"
" gzip > %(outf_con)s")
P.run()
# sort infile by column and write top nPeaks_max to outfile (optimum)
ignore_pipe_errors = True
statement = ("zcat %(infile)s |"
" %(sort_statement)s |"
" head -%(nPeaks_max)s |"
" gzip > %(outf_opt)s")
P.run()
def qcSummary(infiles, outfile):
'''create a summary table of relevant QC metrics'''
# Some QC metrics are specific to paired end data
if PAIRED:
exclude = []
paired_columns = '''READ_PAIRS_EXAMINED as no_pairs,
PERCENT_DUPLICATION as pct_duplication,
ESTIMATED_LIBRARY_SIZE as library_size,
PCT_READS_ALIGNED_IN_PAIRS
as pct_reads_aligned_in_pairs,
MEDIAN_INSERT_SIZE
as median_insert_size,
'''
pcat = "PAIR"
else:
exclude = ["qc_library_complexity", "qc_insert_size_metrics"]
paired_columns = ''
pcat = "UNPAIRED"
tables = [P.toTable(x) for x in infiles
if P.toTable(x) not in exclude]
t1 = tables[0]
name_fields = PARAMS["name_field_titles"].strip()
stat_start = '''select distinct %(name_fields)s,
sample_information.sample_id,
fraction_spliced,
fraction_spike,
qc_no_genes_cufflinks.protein_coding
as cufflinks_no_genes_pc,
qc_no_genes_cufflinks.total
as cufflinks_no_genes,
qc_no_genes_featurecounts.protein_coding
as featurecounts_no_genes_pc,
qc_no_genes_featurecounts.total
as featurecounts_no_genes,
three_prime_bias
as three_prime_bias,
nreads_uniq_map_genome,
nreads_uniq_map_spike,
%(paired_columns)s
PCT_MRNA_BASES
as pct_mrna,
PCT_CODING_BASES
as pct_coding,
PCT_PF_READS_ALIGNED
as pct_reads_aligned,
TOTAL_READS
as total_reads,
PCT_ADAPTER
as pct_adapter,
PF_HQ_ALIGNED_READS*1.0/PF_READS
as pct_pf_reads_aligned_hq
from %(t1)s
''' % locals()
join_stat = ""
for table in tables[1:]:
join_stat += "left join " + table + "\n"
join_stat += "on " + t1 + ".sample_id=" + table + ".sample_id\n"
where_stat = '''where qc_alignment_summary_metrics.CATEGORY="%(pcat)s"
''' % locals()
statement = "\n".join([stat_start, join_stat, where_stat])
df = DB.fetch_DataFrame(statement, PARAMS["database_name"])
df.to_csv(outfile, sep="\t", index=False)
def generatePeakSets(infile, outfiles):
outf_con, outf_opt = outfiles
# retrieve maximum number of peaks obtained from inter-replicate IDR
# (table created by loadNPeaksForIndividualReplicates)
statement = ("SELECT"
" Experiment,"
" max(n_peaks) AS nPeaks"
" FROM individual_replicates_nPeaks"
" GROUP BY experiment")
df = Database.fetch_DataFrame(statement)
# reassign experiment as index
df = df.set_index("Experiment")
# retrieve number of peaks obtained from pooled_pseudoreplicate IDR
# (table created by loadNPeaksForPooledPseudoreplicates)
statement = ("SELECT"
" Experiment,"
" n_peaks AS nPeaks"
" FROM pooled_pseudoreplicates_nPeaks")
df2 = Database.fetch_DataFrame(statement)
# reassign experiment as index
df2 = df2.set_index("Experiment")
# split the infile name to obtain experiment
sample_id = os.path.basename(infile).split("_VS_")[0]
sample = sample_id.split("-")
experiment = "_".join([sample[0], sample[1]])
# retrieve max_numPeaks for experiment
nPeaks = int(df.loc[experiment])
# retrieve numPeaks_Rep0 for experiment
nPeaks_rep0 = int(df2.loc[experiment])
# retrieve maximumn of the two
nPeaks_max = max(nPeaks, nPeaks_rep0)
# establish which column to sort by
if PARAMS["idr_options_ranking_measure"] == "signal.value":
sort_statement = "sort -k7nr,7nr"
elif PARAMS["idr_options_ranking_measure"] == "p.value":
sort_statement = "sort -k8nr,8nr"
elif PARAMS["idr_options_ranking_measure"] == "q.value":
sort_statement = "sort -k9nr,9nr"
else:
raise ValueError("Unrecognised ranking_measure"
" %s don't know which column"
" to sort on" % PARAMS["idr_options_ranking_measure"])
# sort infile by column and write top nPeaks to outfile (conservative)
ignore_pipe_errors = True
statement = ("zcat %(infile)s |"
" %(sort_statement)s |"
" head -%(nPeaks)s |"
" gzip > %(outf_con)s")
P.run()
# sort infile by column and write top nPeaks_max to outfile (optimum)
ignore_pipe_errors = True
statement = ("zcat %(infile)s |"
" %(sort_statement)s |"
" head -%(nPeaks_max)s |"
" gzip > %(outf_opt)s")
P.run()
def qcSummary(infiles, outfile):
'''create a summary table of relevant QC metrics'''
# Some QC metrics are specific to paired end data
if PAIRED:
exclude = []
paired_columns = '''READ_PAIRS_EXAMINED as no_pairs,
PERCENT_DUPLICATION as pct_duplication,
ESTIMATED_LIBRARY_SIZE as library_size,
PCT_READS_ALIGNED_IN_PAIRS
as pct_reads_aligned_in_pairs,
MEDIAN_INSERT_SIZE
as median_insert_size,
'''
pcat = "PAIR"
else:
exclude = ["qc_library_complexity", "qc_insert_size_metrics"]
paired_columns = ''
pcat = "UNPAIRED"
tables = [P.toTable(x) for x in infiles if P.toTable(x) not in exclude]
t1 = tables[0]
name_fields = PARAMS["name_field_titles"].strip()
stat_start = '''select distinct %(name_fields)s,
sample_information.sample_id,
fraction_spliced,
fraction_spike,
qc_no_genes_cufflinks.protein_coding
as cufflinks_no_genes_pc,
qc_no_genes_cufflinks.total
as cufflinks_no_genes,
qc_no_genes_featurecounts.protein_coding
as featurecounts_no_genes_pc,
qc_no_genes_featurecounts.total
as featurecounts_no_genes,
three_prime_bias
as three_prime_bias,
nreads_uniq_map_genome,
nreads_uniq_map_spike,
%(paired_columns)s
PCT_MRNA_BASES
as pct_mrna,
PCT_CODING_BASES
as pct_coding,
PCT_PF_READS_ALIGNED
as pct_reads_aligned,
TOTAL_READS
as total_reads,
PCT_ADAPTER
as pct_adapter,
PF_HQ_ALIGNED_READS*1.0/PF_READS
as pct_pf_reads_aligned_hq
from %(t1)s
''' % locals()
join_stat = ""
for table in tables[1:]:
join_stat += "left join " + table + "\n"
join_stat += "on " + t1 + ".sample_id=" + table + ".sample_id\n"
where_stat = '''where qc_alignment_summary_metrics.CATEGORY="%(pcat)s"
''' % locals()
statement = "\n".join([stat_start, join_stat, where_stat])
df = DB.fetch_DataFrame(statement, PARAMS["database_name"])
df.to_csv(outfile, sep="\t", index=False)
def defineTads(infile, outfile):
'''
Motif is "forward" if present on + strand, and "reverse" if present on - strand
insulator pairs (from intersection) can therefore have motifs in the following orientations:
1) convergent (F, R)
2) divergent (R, F)
3) same direction + strand (F, F)
4) same direction - strand (R, R)
Intervals generated from peak intersections with motifs in convergent orientation will represent TADs (or subTADS...)
'''
db = PARAMS["database"]
npeaks = PARAMS["tads_npeaks"]
pwidth = PARAMS["tads_pwidth"]
tmp_dir = "$SCRATCH_DIR"
# fetch insulator peaks with fimo motifs
table = "insulators_" + '_'.join([str(npeaks), str(pwidth)
]) + "_fimo_table"
statement = '''select * from %(table)s''' % locals()
motifs = DB.fetch_DataFrame(statement, db)
# get most significant motif for each peak
motifs = motifs.sort_values(["sequence_name", "q_value"],
0).drop_duplicates(subset="sequence_name",
keep="first")
motifs.to_csv("insulators_fimoMotifs.txt", sep="\t",
header=True) # save peaks w/ annotated motifs as df
upload2csvdb(motifs, "insulators_fimoMotifs", db) # upload to csvdb
# get peaks (bed format) corresponding to fimo motifs
statement = '''select b.contig, b.start, b.end, a.sequence_name, b.peak_score, a.strand, a.q_value
from insulators_fimoMotifs a inner join insulators b on a.sequence_name = b.peak_id'''
motif_bed = DB.fetch_DataFrame(statement, db)
motif_bed = motif_bed.sort_values(["sequence_name", "q_value"],
0).drop_duplicates(
subset="sequence_name", keep="first")
motif_bed.to_csv("motif_bed.txt", sep="\t", header=True, index=False)
# merge peaks
# iterate over a range of distances (1mb - 1kb) within which insulators peaks are merged
### descending order of distances -> favours bigger TADs, and joins up remaining intervals up to min. size of 1kb
# merged insulators selected for with awk "," in $6 (strand col) ***Limited to merges of two peaks with F,R orientation with ($6=="\+,-")
# merged insulators written to tmp file (tmp + str(counter))
# for each successive merge after n=1 peaks from previous merge are subtracted from results with bedtools (w/ -A flag to remove entire intervals)
### a few of the later TADs are ver large and are merged over previous, how to correct for this? merge final file (only overlapping tads?)
# n = 0
# distances = range(0, 10100000, 10000) # 10mb to 1kb, 10kb decreases
# distances = distances[::-1] # invert list -> descending order
# for dist in distances:
# n = n +1
# tmp = "tmp" + str(n)
# if n == 1:
# statement = '''tmp=`mktemp -p %(tmp_dir)s`; checkpoint;
# tail -n+2 motif_bed.txt |
# sort -k1,1 -k2,2n - > $tmp; checkpoint;
# mergeBed -c 4,5,6,7 -o collapse,mean,collapse,mean -d %(dist)s -i $tmp |
# awk 'BEGIN {OFS="\\t"} {if ($6 == "\+,-") print $0}' - > %(tmp)s''' % locals()
# elif n > 1 and n < len(distances):
# merge = tmp.replace(str(n), str(n-1))
# statement = '''tmp=`mktemp -p %(tmp_dir)s`; checkpoint;
# tail -n+2 motif_bed.txt |
# sort -k1,1 -k2,2n - |
# mergeBed -c 4,5,6,7 -o collapse,mean,collapse,mean -d %(dist)s -i - |
# awk 'BEGIN {OFS="\\t"} {if ($6 == "\+,-") print $0}' - > $tmp; checkpoint;
# subtractBed -A -a $tmp -b %(merge)s > %(tmp)s''' % locals()
# elif n == len(distances):
# merge = tmp.replace(str(n), str(n-1))
# statement = '''tmp=`mktemp -p %(tmp_dir)s`; checkpoint;
# tail -n+2 motif_bed.txt |
# sort -k1,1 -k2,2n - |
# mergeBed -c 4,5,6,7 -o collapse,mean,collapse,mean -d %(dist)s -i - |
# awk 'BEGIN {OFS="\\t"} {if ($6 == "\+,-") print $0}' - > $tmp; checkpoint;
# subtractBed -A -a $tmp -b %(merge)s > %(tmp)s; checkpoint;
# awk 'BEGIN {OFS="\\t"} {if ($3-$2 > 1000) print $0}' <(cat tmp*) |
# sort -k1,1 -k2,2n - |
# mergeBed -c 4,5,6,7 -o collapse,mean,collapse,mean -i - > %(outfile)s; checkpoint;
# rm tmp*''' % locals()
### Instead of merging peaks with F/R motif orientation I could seperate insulator peaks into F & R files,
### then use bedtools closest to intersect peaks up to a max distance of n & remove peaks with divergent motifs.
# Ensure "closest" matches are on the same chromosome with awk, also remove features > 1mb wide
statement = '''tmp=`mktemp -p %(tmp_dir)s`; checkpoint;
Fstrand=`mktemp -p %(tmp_dir)s`; checkpoint;
Rstrand=`mktemp -p %(tmp_dir)s`; checkpoint;
awk 'BEGIN {OFS="\\t"} {if ($6 == "+") print $0}' <(tail -n+2 motif_bed.txt | sort -k1,1 -k2,2n ) > $Fstrand; checkpoint;
awk 'BEGIN {OFS="\\t"} {if ($6 == "-") print $0}' <(tail -n+2 motif_bed.txt | sort -k1,1 -k2,2n ) > $Rstrand; checkpoint;
~/devel/GIT/bedtools2/bin/closestBed -iu -D ref
-a $Fstrand
-b $Rstrand
> $tmp; checkpoint;
awk 'BEGIN {OFS="\\t"} {if ($1 == $8 && $9-$2 < 1000000) print $1,$2,$9,$4"/"$11,($5+$12)/2,$6","$13,($7+$14)/2}' $tmp > %(outfile)s '''
### This works better!
# Need to incoporate CTCF & cohesin coverage over candidate insulators. Then filter out insulator pairs (candidate TADS) with large discrepancies in ChIP signal
# Czimmerer et al use a cut off of > 2fold difference betweeen start & end peaks of TADS in ChIP signal
# Add ChIP coverage code for insulator peaks & save to db, then incoporate CTCF & cohesin signal into awk filter at the end of this statement
print statement
P.run()
